If the power fc was tuned to counter airleaks and now you have a plenum with no leaks, then a re-tune will fix your problems. Also black smoke is ok, just means the tune is a bit rich, probably stuffed from when you changed the plenum. I recently cracked my intercooler and now it leaks which stuffed my tune the same as yours. Now it blows black smoke too cos its running rich. Its blue smoke that you want to look out for, blue is never good.
Hope that made sense. Good luck with the car mate